Package | Description |
---|---|
com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
|
com.compomics.util.experiment.identification.amino_acid_tags.matchers |
Tag matching classes.
|
com.compomics.util.experiment.identification.matches |
Experiment classes related to matches.
|
com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
|
com.compomics.util.experiment.identification.protein_inference.fm_index |
Protein sequence database indexing classes based on Burrows-Wheeler transform.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<ModificationMatch> |
Peptide.getModificationMatches()
Getter for the modifications carried by this peptide.
|
HashMap<Integer,ArrayList<ModificationMatch>> |
AminoAcidSequence.getModificationMatches()
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
|
HashMap<Integer,ArrayList<ModificationMatch>> |
AminoAcidPattern.getModificationMatches()
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
|
ArrayList<ModificationMatch> |
AminoAcidSequence.getModificationsAt(int localization)
Returns the modifications found at a given localization.
|
ArrayList<ModificationMatch> |
AminoAcidPattern.getModificationsAt(int localization)
Returns the modifications found at a given localization.
|
Modifier and Type | Method and Description |
---|---|
void |
AminoAcidSequence.addModificationMatch(int localization,
ModificationMatch modificationMatch)
Adds a modification to one of the amino acid sequence.
|
void |
AminoAcidPattern.addModificationMatch(int localization,
ModificationMatch modificationMatch)
Adds a modification to one of the amino acid pattern.
|
void |
Peptide.addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match.
|
void |
AminoAcidSequence.changeModificationSite(ModificationMatch modificationMatch,
int oldLocalization,
int newLocalization)
Changes the localization of a modification match.
|
void |
AminoAcidPattern.changeModificationSite(ModificationMatch modificationMatch,
int oldLocalization,
int newLocalization)
Changes the localization of a modification match.
|
void |
AminoAcidSequence.removeModificationMatch(int localisation,
ModificationMatch modificationMatch)
Removes a modification match in the given sequence.
|
void |
AminoAcidPattern.removeModificationMatch(int localisation,
ModificationMatch modificationMatch)
Removes a modification match in the given pattern.
|
Modifier and Type | Method and Description |
---|---|
void |
AminoAcidSequence.addModificationMatches(int localization,
ArrayList<ModificationMatch> modificationMatches)
Adds a list of modifications to one of the amino acid sequence.
|
void |
AminoAcidPattern.addModificationMatches(int localization,
ArrayList<ModificationMatch> modificationMatches)
Adds a list of modifications to one of the amino acid pattern.
|
static String |
Peptide.getKey(String sequence,
ArrayList<ModificationMatch> modificationMatches)
Returns the reference key of a peptide.
|
void |
Peptide.setModificationMatches(ArrayList<ModificationMatch> modificationMatches)
Sets new modification matches for the peptide.
|
Constructor and Description |
---|
AminoAcidSequence(String sequence,
HashMap<Integer,ArrayList<ModificationMatch>> modifications)
Constructor taking a sequence of amino acids as input.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications)
Constructor.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications,
ArrayList<VariantMatch> variants,
boolean sanityCheck)
Constructor for the peptide.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications,
boolean sanityCheck)
Constructor.
|
Peptide(String aSequence,
ArrayList<ModificationMatch> modifications,
boolean sanityCheck,
Double mass)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
TagMatcher.buildPeptides(String accession,
String sequence,
ArrayList<SequenceSegment> nTermPossibleSequences,
String seedSequence,
ArrayList<SequenceSegment> cTermPossibleSequences,
HashMap<Integer,ArrayList<ModificationMatch>> modificationsAtIndex,
int mutationsAtIndex)
Builds the possible peptides based on the given terminal segments and the
seed sequence.
|
Modifier and Type | Method and Description |
---|---|
ModificationMatch |
ModificationMatch.clone()
Clones the modification match into a new match with the same attributes.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ModificationMatch.isSameAs(ModificationMatch anotherModificationMatch)
Indicates whether this modification match is the same of another one.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<ModificationMatch> |
PeptideProteinMapping.getModificationMatches()
Returns eventual modifications found.
|
Constructor and Description |
---|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ArrayList<ModificationMatch> modificationMatches)
Constructor.
|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ArrayList<ModificationMatch> modificationMatches,
ArrayList<VariantMatch> variantMatches)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
ModificationMatch |
MatrixContent.modification
Index to the modifications list.
|
Modifier and Type | Field and Description |
---|---|
ArrayList<ModificationMatch> |
MatrixContent.modifications
List of all modifications.
|
Constructor and Description |
---|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int[] numSpecificVariants,
char variant,
String allVariants)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int numVariants,
char variant,
String allVariants)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
String peptideSequenceSearch,
int length,
int numX,
int tagComponent,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
String peptideSequenceSearch,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int ambiguousChar)
Constructor.
|
Constructor and Description |
---|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int[] numSpecificVariants,
char variant,
String allVariants)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int numVariants,
char variant,
String allVariants)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
String peptideSequenceSearch,
int length,
int numX,
int tagComponent,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos)
Constructor.
|
MatrixContent(int left,
int right,
int character,
MatrixContent previousContent,
double mass,
String peptideSequence,
String peptideSequenceSearch,
int length,
int numX,
ModificationMatch modification,
ArrayList<ModificationMatch> modifications,
int modifictationPos,
int ambiguousChar)
Constructor.
|
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